Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-13 11:32:14 -0400 (Mon, 13 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1970/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpatialDecon 1.15.0 (landing page) Maddy Griswold
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the SpatialDecon package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: SpatialDecon |
Version: 1.15.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialDecon_1.15.0.tar.gz |
StartedAt: 2024-05-13 03:57:40 -0400 (Mon, 13 May 2024) |
EndedAt: 2024-05-13 04:08:18 -0400 (Mon, 13 May 2024) |
EllapsedTime: 637.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SpatialDecon.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialDecon_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/SpatialDecon.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpatialDecon/DESCRIPTION’ ... OK * this is package ‘SpatialDecon’ version ‘1.15.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SpatialDecon’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE download_profile_matrix: no visible binding for global variable ‘profile_matrix’ Undefined global functions or variables: profile_matrix * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed runCollapseCellTypes 77.922 2.722 81.149 runReverseDecon 77.199 2.705 80.536 runspatialdecon 56.944 2.048 60.554 runMergeTumorIntoX 15.495 0.202 15.768 runErrorModel 14.736 0.144 14.947 reverseDecon 6.863 0.222 7.110 SpatialDecon-package 5.446 0.090 5.559 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/SpatialDecon.Rcheck/00check.log’ for details.
SpatialDecon.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpatialDecon ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘SpatialDecon’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SpatialDecon)
SpatialDecon.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(SpatialDecon) > > test_check("SpatialDecon") [1] "Creating Atlas" [1] "1 / 4 : B" [1] "2 / 4 : C" [1] "3 / 4 : A" [1] "4 / 4 : D" [ FAIL 0 | WARN 0 | SKIP 0 | PASS 96 ] > > proc.time() user system elapsed 169.052 6.216 178.199
SpatialDecon.Rcheck/SpatialDecon-Ex.timings
name | user | system | elapsed | |
SpatialDecon-package | 5.446 | 0.090 | 5.559 | |
TIL_barplot | 1.611 | 0.035 | 1.666 | |
collapseCellTypes | 1.592 | 0.023 | 1.619 | |
create_profile_matrix | 0.864 | 0.023 | 0.896 | |
derive_GeoMx_background | 0.004 | 0.002 | 0.011 | |
download_profile_matrix | 0.248 | 0.336 | 2.063 | |
florets | 1.371 | 0.040 | 1.421 | |
mergeTumorIntoX | 0.013 | 0.003 | 0.016 | |
reverseDecon | 6.863 | 0.222 | 7.110 | |
runCollapseCellTypes | 77.922 | 2.722 | 81.149 | |
runErrorModel | 14.736 | 0.144 | 14.947 | |
runMergeTumorIntoX | 15.495 | 0.202 | 15.768 | |
runReverseDecon | 77.199 | 2.705 | 80.536 | |
runspatialdecon | 56.944 | 2.048 | 60.554 | |
spatialdecon | 4.602 | 0.159 | 4.781 | |